Canonical Poly(A) Polymerase Activity Promotes the Decay of a Wide Variety of Mammalian Nuclear RNAs

Stefan M. Bresson, Olga V. Hunter, Allyson C. Hunter, Nicholas K. Conrad

Research output: Contribution to journalArticle

33 Citations (Scopus)

Abstract

The human nuclear poly(A)-binding protein PABPN1 has been implicated in the decay of nuclear noncoding RNAs (ncRNAs). In addition, PABPN1 promotes hyperadenylation by stimulating poly(A)-polymerases (PAPα/γ), but this activity has not previously been linked to the decay of endogenous transcripts. Moreover, the mechanisms underlying target specificity have remained elusive. Here, we inactivated PAP-dependent hyperadenylation in cells by two independent mechanisms and used an RNA-seq approach to identify endogenous targets. We observed the upregulation of various ncRNAs, including snoRNA host genes, primary miRNA transcripts, and promoter upstream antisense RNAs, confirming that hyperadenylation is broadly required for the degradation of PABPN1-targets. In addition, we found that mRNAs with retained introns are susceptible to PABPN1 and PAPα/γ-mediated decay (PPD). Transcripts are targeted for degradation due to inefficient export, which is a consequence of reduced intron number or incomplete splicing. Additional investigation showed that a genetically-encoded poly(A) tail is sufficient to drive decay, suggesting that degradation occurs independently of the canonical cleavage and polyadenylation reaction. Surprisingly, treatment with transcription inhibitors uncouples polyadenylation from decay, leading to runaway hyperadenylation of nuclear decay targets. We conclude that PPD is an important mammalian nuclear RNA decay pathway for the removal of poorly spliced and nuclear-retained transcripts.

Original languageEnglish (US)
Article numbere1005610
JournalPLoS Genetics
Volume11
Issue number10
DOIs
StatePublished - 2015

Fingerprint

Polynucleotide Adenylyltransferase
Nuclear RNA
Untranslated RNA
Polyadenylation
Introns
Radioactivity
RNA
Poly(A)-Binding Proteins
deterioration
Small Nucleolar RNA
Homeless Youth
Antisense RNA
Messenger RNA
RNA Stability
MicroRNAs
Up-Regulation
degradation
Genes
introns
cleavage

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology
  • Ecology, Evolution, Behavior and Systematics
  • Cancer Research
  • Genetics(clinical)

Cite this

Canonical Poly(A) Polymerase Activity Promotes the Decay of a Wide Variety of Mammalian Nuclear RNAs. / Bresson, Stefan M.; Hunter, Olga V.; Hunter, Allyson C.; Conrad, Nicholas K.

In: PLoS Genetics, Vol. 11, No. 10, e1005610, 2015.

Research output: Contribution to journalArticle

Bresson, Stefan M. ; Hunter, Olga V. ; Hunter, Allyson C. ; Conrad, Nicholas K. / Canonical Poly(A) Polymerase Activity Promotes the Decay of a Wide Variety of Mammalian Nuclear RNAs. In: PLoS Genetics. 2015 ; Vol. 11, No. 10.
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